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Kersten C, Archambault P, Köhler LP. Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. J Chem Inf Model 2024; 64:4485-4499. [PMID: 38766733 DOI: 10.1021/acs.jcim.4c00520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.
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Affiliation(s)
- Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg-University, BioZentrum I, Hanns-Dieter-Hüsch.Weg 15, 55128 Mainz, Germany
| | - Philippe Archambault
- Chemical Computing Group, 910-1010 Sherbrooke W., Montreal, Quebec, Canada H3A 2R7
| | - Luca P Köhler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
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2
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Fedorova O, Arhin G, Pyle AM, Frank AT. In Silico Discovery of Group II Intron RNA Splicing Inhibitors. ACS Chem Biol 2023; 18:1968-1975. [PMID: 37602469 DOI: 10.1021/acschembio.3c00160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Here, we describe the discovery of compounds that inhibit self-splicing in group II introns. Using docking calculations, we targeted the catalytic active site within the Oceanobacillus iheyensis group IIC intron and virtually screened a library of lead-like compounds. From this initial virtual screen, we identified three unique scaffolds that inhibit splicing in vitro. Additional tests revealed that an analog of the lead scaffold inhibits splicing in an intron-dependent manner. Furthermore, this analog exhibited activity against the group II intron from a different class: the yeast ai5γ IIB intron. The splicing inhibitors we identified could serve as chemical tools for developing group II intron-targeted antifungals, and, more broadly, our results highlight the potential of in silico techniques for identifying bioactive hits against structured and functionally complex RNAs.
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Affiliation(s)
| | - Grace Arhin
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Aaron T Frank
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Morishita EC. Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies. Expert Opin Drug Discov 2023; 18:207-226. [PMID: 36322542 DOI: 10.1080/17460441.2022.2134852] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The field of RNA-targeted small molecules is rapidly evolving, owing to the advances in experimental and computational technologies. With the identification of several bioactive small molecules that target RNA, including the FDA-approved risdiplam, the biopharmaceutical industry is gaining confidence in the field. This review, based on the literature obtained from PubMed, aims to disseminate information about the various technologies developed for targeting RNA with small molecules and propose areas for improvement to develop drugs more efficiently, particularly those linked to diseases with unmet medical needs. AREAS COVERED The technologies for the identification of RNA targets, screening of chemical libraries against RNA, assessing the bioactivity and target engagement of the hit compounds, structure determination, and hit-to-lead optimization are reviewed. Along with the description of the technologies, their strengths, limitations, and examples of how they can impact drug discovery are provided. EXPERT OPINION Many existing technologies employed for protein targets have been repurposed for use in the discovery of RNA-targeted small molecules. In addition, technologies tailored for RNA targets have been developed. Nevertheless, more improvements are necessary, such as artificial intelligence to dissect important RNA structures and RNA-small-molecule interactions and more powerful chemical probing and structure prediction techniques.
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Kallert E, Fischer TR, Schneider S, Grimm M, Helm M, Kersten C. Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ 1-Riboswitch. J Chem Inf Model 2022; 62:4134-4148. [PMID: 35994617 DOI: 10.1021/acs.jcim.2c00751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced during docking, namely, protomer and tautomer selection, target dynamics, and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective VS with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Simon Schneider
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Maike Grimm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
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5
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fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLoS Comput Biol 2022; 18:e1009783. [PMID: 35653385 PMCID: PMC9197077 DOI: 10.1371/journal.pcbi.1009783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/14/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Computational methods play a pivotal role in drug discovery and are widely applied in virtual screening, structure optimization, and compound activity profiling. Over the last decades, almost all the attention in medicinal chemistry has been directed to protein-ligand binding, and computational tools have been created with this target in mind. With novel discoveries of functional RNAs and their possible applications, RNAs have gained considerable attention as potential drug targets. However, the availability of bioinformatics tools for nucleic acids is limited. Here, we introduce fingeRNAt—a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands. The program detects nine types of interactions: (i) hydrogen and (ii) halogen bonds, (iii) cation-anion, (iv) pi-cation, (v) pi-anion, (vi) pi-stacking, (vii) inorganic ion-mediated, (viii) water-mediated, and (ix) lipophilic interactions. However, the scope of detected interactions can be easily expanded using a simple plugin system. In addition, detected interactions can be visualized using the associated PyMOL plugin, which facilitates the analysis of medium-throughput molecular complexes. Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt)—a binary string where the respective bit in the fingerprint is set to 1 if a particular interaction is present and to 0 otherwise. This output format, in turn, enables high-throughput analysis of interaction data using data analysis techniques. We present applications of fingeRNAt-generated interaction fingerprints for visual and computational analysis of RNA-ligand complexes, including analysis of interactions formed in experimentally determined RNA-small molecule ligand complexes deposited in the Protein Data Bank. We propose interaction fingerprint-based similarity as an alternative measure to RMSD to recapitulate complexes with similar interactions but different folding. We present an application of interaction fingerprints for the clustering of molecular complexes. This approach can be used to group ligands that form similar binding networks and thus have similar biological properties. The fingeRNAt software is freely available at https://github.com/n-szulc/fingeRNAt.
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6
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Role and Perspective of Molecular Simulation-Based Investigation of RNA-Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding. Molecules 2021; 26:molecules26113384. [PMID: 34205049 PMCID: PMC8199858 DOI: 10.3390/molecules26113384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.
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7
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Chopra B, Dhingra AK. Natural products: A lead for drug discovery and development. Phytother Res 2021; 35:4660-4702. [PMID: 33847440 DOI: 10.1002/ptr.7099] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 12/29/2022]
Abstract
Natural products are used since ancient times in folklore for the treatment of various ailments. Plant-derived products have been recognized for many years as a source of therapeutic agents and structural diversity. A literature survey has been carried out to determine the utility of natural molecules and their modified analogs or derivatives as pharmacological active entities. This review presents a study on the importance of natural products in terms of drug discovery and development. It describes how the natural components can be utilized after small modifications in new perspectives. Various new modifications in structure offer a unique opportunity to establish a new molecular entity with better pharmacological potential. It was concluded that in this current era, new attempts are taken to utilize the compounds derived from natural sources as novel drug candidates, with a focus to find and discover new effective molecules that were referred to as "new entities of natural product drug discovery."
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Affiliation(s)
- Bhawna Chopra
- Department of Pharmaceutical Chemistry, Guru Gobind Singh College of Pharmacy, Yamuna Nagar, India
| | - Ashwani Kumar Dhingra
- Department of Pharmaceutical Chemistry, Guru Gobind Singh College of Pharmacy, Yamuna Nagar, India
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8
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Stefaniak F, Bujnicki JM. AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. PLoS Comput Biol 2021; 17:e1008309. [PMID: 33524009 PMCID: PMC7877745 DOI: 10.1371/journal.pcbi.1008309] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/11/2021] [Accepted: 12/16/2020] [Indexed: 11/22/2022] Open
Abstract
RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets. The performance of these methods, when applied to RNA-ligand systems, is insufficient. To overcome these problems, we developed AnnapuRNA, a new knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method. We also evaluated three main factors that may influence the structure prediction, i.e., the starting conformer of a ligand, the docking program, and the scoring function used. We applied the AnnapuRNA method for a post-hoc study of the recently published structures of the FMN riboswitch. Software is available at https://github.com/filipspl/AnnapuRNA. Drug development is a lengthy and complicated process, which requires costly experiments on a very large number of chemical compounds. The identification of chemical molecules with desired properties can be facilitated by computational methods. Several methods were developed for computer-aided design of drugs that target protein molecules. However, recently the ribonucleic acid (RNA) emerged as an attractive target for the development of new drugs. Unfortunately, the portfolio of the computer methods that can be applied to study RNA and its interactions with small chemical molecules is very limited. This situation motivated us to develop a new computational method, with which to predict RNA-small molecule interactions. To this end, we collected the information on the statistics of interactions in experimentally determined structures of complexes formed by RNA with small molecules. We then used the statistical data to train machine learning methods aiming to distinguish between RNA-ligand interactions observed experimentally and other interactions that can be observed in theoretical analyses, but are not observed in nature. The resulting method called AnnapuRNA is superior to other similar tools and can be used to predict preferred ligands of RNA molecules and how RNA and small molecules interact with each other.
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Affiliation(s)
- Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
- * E-mail: (FS); (JMB)
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
- * E-mail: (FS); (JMB)
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9
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Hewitt WM, Calabrese DR, Schneekloth JS. Evidence for ligandable sites in structured RNA throughout the Protein Data Bank. Bioorg Med Chem 2019; 27:2253-2260. [PMID: 30982658 PMCID: PMC8283815 DOI: 10.1016/j.bmc.2019.04.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
Abstract
RNA has attracted considerable attention as a target for small molecules. However, methods to identify, study, and characterize suitable RNA targets have lagged behind strategies for protein targets. One approach that has received considerable attention for protein targets has been to utilize computational analysis to investigate ligandable "pockets" on proteins that are amenable to small molecule binding. These studies have shown that selected physical properties of pockets are important parameters that govern the ability of a structure to bind to small molecules. This work describes a similar analysis to study pockets on all RNAs in the Protein Data Bank (PDB). Using parameters such as buriedness, hydrophobicity, volume, and other properties, the set of all RNAs is analyzed and compared to all proteins. Considerable overlap is observed between the properties of pockets on RNAs and proteins. Thus, many RNAs are capable of populating conformations with pockets that are likely suitable for small molecule binding. Further, principal moment of inertia (PMI) calculations reveal that liganded RNAs exist in diverse structural space, much of which overlaps with protein structural space. Taken together, these results suggest that complex folded RNAs adopt unique structures with pockets that may represent viable opportunities for small molecule targeting.
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Affiliation(s)
- William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States.
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10
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Integrated Chemoinformatics Approaches Toward Epigenetic Drug Discovery. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [DOI: 10.1007/978-3-030-05282-9_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
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Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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12
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Structure-Based Discovery of Small Molecules Binding to RNA. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_29] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Bhoye D, Behera AK, Cherian SS. A molecular modelling approach to understand the effect of co-evolutionary mutations (V344M, I354L) identified in the PB2 subunit of influenza A 2009 pandemic H1N1 virus on m7GTP ligand binding. J Gen Virol 2016; 97:1785-1796. [PMID: 27154164 DOI: 10.1099/jgv.0.000500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The cap binding domain of the polymerase basic 2 (PB2) subunit of influenza polymerases plays a critical role in mediating the 'cap-snatching' mechanism by binding the 5' cap of host pre-mRNAs during viral mRNA transcription. Monitoring variations in the PB2 protein is thus vital for evaluating the pathogenic potential of the virus. Based on selection pressure analysis of PB2 gene sequences of the pandemic H1N1 (pH1N1) viruses of the period 2009-2014, we identified a site, 344V/M, in the vicinity of the cap binding pocket showing evidence of adaptive evolution and another co-evolving residue, 354I/L, in close vicinity. Modelling of the three-dimensional structure of the pH1N1 PB2 cap binding domain, docking of the pre-mRNA cap analogue m7GTP and molecular dynamics simulation studies of the docked complexes performed for four PB2 variants observed showed that the complex possessing V344M with I354L possessed better ligand binding affinity due to additional hydrogen bond contacts between m7GTP and the key residues His432 and Arg355 that was attributed to a displacement of the 424 loop and a flip of the side chain of Arg355, respectively. The co-evolutionary mutations identified (V344M, I354L) were found to be established in the PB2 gene of the pH1N1 viral population over the period 2010-2014. The study demonstrates the molecular basis for the enhanced m7GTP ligand binding affinity with the 344M-354L synergistic combination in PB2. Furthermore, the insight gained into understanding the molecular mechanism of cap binding in pH1N1 viruses may be useful for designing novel drugs targeting the PB2 cap binding domain.
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Affiliation(s)
- Dipali Bhoye
- Bioinformatics and Data Management Group, National Institute of Virology, Pune 411001, Maharashtra, India
| | - Abhisek Kumar Behera
- Bioinformatics and Data Management Group, National Institute of Virology, Pune 411001, Maharashtra, India
| | - Sarah S Cherian
- Bioinformatics and Data Management Group, National Institute of Virology, Pune 411001, Maharashtra, India
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14
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Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Characterization and in vitro activity of a branched peptide boronic acid that interacts with HIV-1 RRE RNA. Bioorg Med Chem 2016; 24:3947-3952. [PMID: 27091070 DOI: 10.1016/j.bmc.2016.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
A branched peptide containing multiple boronic acids was found to bind RRE IIB selectively and inhibit HIV-1 p24 capsid production in a dose-dependent manner. Structure-activity relationship studies revealed that branching in the peptide is crucial for the low micromolar binding towards RRE IIB, and the peptide demonstrates selectivity towards RRE IIB in the presence of tRNA. Footprinting studies suggest a binding site on the upper stem and internal loop regions of the RNA, which induces enzymatic cleavage of the internal loops of RRE IIB upon binding.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Denis M Tebit
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Laurie R Gray
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - David Rekosh
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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15
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Stefaniak F, Chudyk EI, Bodkin M, Dawson WK, Bujnicki JM. Modeling of ribonucleic acid-ligand interactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1226] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw Poland
| | - Ewa I. Chudyk
- Research Informatics; Evotec (UK) Ltd; Milton Park UK
| | | | - Wayne K. Dawson
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
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16
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Wynn JE, Santos WL. HIV-1 drug discovery: targeting folded RNA structures with branched peptides. Org Biomol Chem 2015; 13:5848-58. [PMID: 25958855 PMCID: PMC4511164 DOI: 10.1039/c5ob00589b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA.
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17
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Behera AK, Basu S, Cherian SS. Molecular mechanism of the enhanced viral fitness contributed by secondary mutations in the hemagglutinin protein of oseltamivir resistant H1N1 influenza viruses: modeling studies of antibody and receptor binding. Gene 2014; 557:19-27. [PMID: 25479009 DOI: 10.1016/j.gene.2014.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 11/25/2022]
Abstract
The envelope protein hemagglutinin (HA) of influenza viruses is primarily associated with host antibody and receptor interactions. The HA protein is known to maintain a functional balance with neuraminidase (NA), the other major envelope protein. Prior to 2007-2008, human seasonal H1N1 viruses possessing the NA H274Y mutation, which confers oseltamivir resistance, generally had low growth capability. Subsequently, secondary mutations that compensate for the deleterious effect of the NA H274Y mutation have been identified. The molecular mechanism of how the defect could be counteracted by these secondary mutations is not fully understood. We studied here the effect of three such mutations (T86K, K144E and R192K) in the HA protein, which are located at either the HA receptor binding site or in the H1N1 antigenic sites. Molecular docking and dynamics studies showed that, of the three mutations, the R192K mutation could have mediated neutralizing antibody escape and decreased receptor binding affinity, either or both of which may have contributed to increased viral fitness. The study suggests the molecular basis of enhanced viral fitness induced by secondary mutations in the evolution of oseltamivir-resistant influenza strains.
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Affiliation(s)
- Abhisek Kumar Behera
- Bioinformatics Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India.
| | - Sushmita Basu
- Bioinformatics Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India.
| | - Sarah S Cherian
- Bioinformatics Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India.
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18
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Zhang W, Bryson DI, Crumpton JB, Wynn J, Santos WL. Targeting folded RNA: a branched peptide boronic acid that binds to a large surface area of HIV-1 RRE RNA. Org Biomol Chem 2014; 11:6263-71. [PMID: 23925474 DOI: 10.1039/c3ob41053f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On-bead high-throughput screening of a medium-sized (1000-2000 Da) branched peptide boronic acid (BPBA) library consisting of 46,656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a K(d) of 1.4 μM with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure-activity studies suggest that the boronic acid moiety and "branching" in peptides are key structural features for efficient binding and selectivity for the folded RNA target. BPBA1 was efficiently taken up by HeLa and A2780 cells. RNA-footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB.
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Affiliation(s)
- Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA
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19
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Disney MD, Yildirim I, Childs-Disney JL. Methods to enable the design of bioactive small molecules targeting RNA. Org Biomol Chem 2014; 12:1029-39. [PMID: 24357181 PMCID: PMC4020623 DOI: 10.1039/c3ob42023j] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RNA is an immensely important target for small molecule therapeutics or chemical probes of function. However, methods that identify, annotate, and optimize RNA-small molecule interactions that could enable the design of compounds that modulate RNA function are in their infancies. This review describes recent approaches that have been developed to understand and optimize RNA motif-small molecule interactions, including structure-activity relationships through sequencing (StARTS), quantitative structure-activity relationships (QSAR), chemical similarity searching, structure-based design and docking, and molecular dynamics (MD) simulations. Case studies described include the design of small molecules targeting RNA expansions, the bacterial A-site, viral RNAs, and telomerase RNA. These approaches can be combined to afford a synergistic method to exploit the myriad of RNA targets in the transcriptome.
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Affiliation(s)
- Matthew D Disney
- The Department of Chemistry, The Scripps Research Institute, 130 Scripps Way #3A1, Jupiter, FL 33458, USA.
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20
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Frączek T, Siwek A, Paneth P. Assessing Molecular Docking Tools for Relative Biological Activity Prediction: A Case Study of Triazole HIV-1 NNRTIs. J Chem Inf Model 2013; 53:3326-42. [DOI: 10.1021/ci400427a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tomasz Frączek
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
| | - Agata Siwek
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
- Department
of Organic Chemistry, Faculty of Pharmacy, Medical University, Chodzki 4a, 20-093 Lublin, Poland
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
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21
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Dos Santos ES, de Souza LCV, de Assis PN, Almeida PF, Ramos-de-Souza E. Novel potential inhibitors for adenylylsulfate reductase to control souring of water in oil industries. J Biomol Struct Dyn 2013; 32:1780-92. [PMID: 24028628 DOI: 10.1080/07391102.2013.834850] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The biogenic production of hydrogen sulfide gas by sulfate-reducing bacteria (SRB) causes serious economic problems for natural gas and oil industry. One of the key enzymes important in this biologic process is adenosine phosphosulfate reductase (APSr). Using virtual screening technique we have discovered 15 compounds that are novel potential APSr inhibitors. Three of them have been selected for molecular docking and microbiological studies which have shown good inhibition of SRB in the produced water from the oil industry.
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Affiliation(s)
- Elias Silva Dos Santos
- a Instituto de Física, Universidade Federal da Bahia , Rua Barão de Geremoabo s/n - Ondina, Salvador , BA , 40.300-000 , Brasil
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22
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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23
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Disney MD. Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts. Drug Discov Today 2013; 18:1228-36. [PMID: 23939337 DOI: 10.1016/j.drudis.2013.07.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 07/26/2013] [Accepted: 07/31/2013] [Indexed: 02/06/2023]
Abstract
RNA is an important yet vastly underexploited target for small molecule chemical probes or lead therapeutics. Small molecules have been used successfully to modulate the function of the bacterial ribosome, viral RNAs and riboswitches. These RNAs are either highly expressed or can be targeted using substrate mimicry, a mainstay in the design of enzyme inhibitors. However, most cellular RNAs are neither highly expressed nor have a lead small molecule inhibitor, a significant challenge for drug discovery efforts. Herein, I describe the design of small molecules targeting expanded repeating transcripts that cause myotonic muscular dystrophy (DM). These test cases illustrate the challenges of designing small molecules that target RNA and the advantages of targeting repeating transcripts. Lastly, I discuss how small molecules might be more advantageous than oligonucleotides for targeting RNA.
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Affiliation(s)
- Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way #3A1, Jupiter, FL 33458, USA.
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24
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Strategies to Block HIV Transcription: Focus on Small Molecule Tat Inhibitors. BIOLOGY 2012; 1:668-97. [PMID: 24832514 PMCID: PMC4009808 DOI: 10.3390/biology1030668] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 01/29/2023]
Abstract
After entry into the target cell, the human immunodeficiency virus type I (HIV) integrates into the host genome and becomes a proviral eukaryotic transcriptional unit. Transcriptional regulation of provirus gene expression is critical for HIV replication. Basal transcription from the integrated HIV promoter is very low in the absence of the HIV transactivator of transcription (Tat) protein and is solely dependent on cellular transcription factors. The 5' terminal region (+1 to +59) of all HIV mRNAs forms an identical stem-bulge-loop structure called the Transactivation Responsive (TAR) element. Once Tat is made, it binds to TAR and drastically activates transcription from the HIV LTR promoter. Mutations in either the Tat protein or TAR sequence usually affect HIV replication, indicating a strong requirement for their conservation. The necessity of the Tat-mediated transactivation cascade for robust HIV replication renders Tat one of the most desirable targets for transcriptional therapy against HIV replication. Screening based on inhibition of the Tat-TAR interaction has identified a number of potential compounds, but none of them are currently used as therapeutics, partly because these agents are not easily delivered for an efficient therapy, emphasizing the need for small molecule compounds. Here we will give an overview of the different strategies used to inhibit HIV transcription and review the current repertoire of small molecular weight compounds that target HIV transcription.
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25
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Chen L, Calin GA, Zhang S. Novel insights of structure-based modeling for RNA-targeted drug discovery. J Chem Inf Model 2012; 52:2741-53. [PMID: 22947071 DOI: 10.1021/ci300320t] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Substantial progress in RNA biology highlights the importance of RNAs (e.g., microRNAs) in diseases and the potential of targeting RNAs for drug discovery. However, the lack of RNA-specific modeling techniques demands the development of new tools for RNA-targeted rational drug design. Herein, we implemented integrated approaches of accurate RNA modeling and virtual screening for RNA inhibitor discovery with the most comprehensive evaluation to date of five docking and 11 scoring methods. For the first time, statistical analysis was heavily employed to assess the significance of our predictions. We found that GOLD:GOLD Fitness and rDock:rDock_solv could accurately predict the RNA ligand poses, and ASP rescoring further improved the ranking of ligand binding poses. Due to the weak correlations (R(2) < 0.3) of existing scoring with experimental binding affinities, we implemented two new RNA-specific scoring functions, iMDLScore1 and iMDLScore2, and obtained better correlations with R(2) = 0.70 and 0.79, respectively. We also proposed a multistep virtual screening approach and demonstrated that rDock:rDock_solv together with iMDLScore2 rescoring obtained the best enrichment on the flexible RNA targets, whereas GOLD:GOLD Fitness combined with rDock_solv rescoring outperformed other methods for rigid RNAs. This study provided practical strategies for RNA modeling and offered new insights into RNA-small molecule interactions for drug discovery.
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Affiliation(s)
- Lu Chen
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, 1901 East Road, Houston Texas 77054, USA
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26
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Dinman JD. Virtual Screening for RNA-Interacting Small Molecules. BIOPHYSICAL APPROACHES TO TRANSLATIONAL CONTROL OF GENE EXPRESSION 2012. [PMCID: PMC7123052 DOI: 10.1007/978-1-4614-3991-2_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Computational virtual screening is useful and powerful strategy for rapid discovery of small biologically active molecules in the early stage of drug discovery. The discovery of a broad range of important biological processes involved by RNA has increased the importance of RNA as a new drug target. To apply structure-based virtual screening methods to the discovery of RNA-binding ligands, many RNA 3D structure prediction programs and optimized docking algorithms have been developed. In this chapter, a number of successful cases of virtual screening targeting RNA will be introduced.
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Affiliation(s)
- Jonathan D. Dinman
- College Park, Cell Biology and Molecular Genetics, University of Maryland, Rm. 2135 Microbiology Building, College Park, 20742-4451 Maryland USA
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27
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Seddon G, Lounnas V, McGuire R, van den Bergh T, Bywater RP, Oliveira L, Vriend G. Drug design for ever, from hype to hope. J Comput Aided Mol Des 2012; 26:137-50. [PMID: 22252446 PMCID: PMC3268973 DOI: 10.1007/s10822-011-9519-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 12/05/2011] [Indexed: 01/28/2023]
Abstract
In its first 25 years JCAMD has been disseminating a large number of techniques aimed at finding better medicines faster. These include genetic algorithms, COMFA, QSAR, structure based techniques, homology modelling, high throughput screening, combichem, and dozens more that were a hype in their time and that now are just a useful addition to the drug-designers toolbox. Despite massive efforts throughout academic and industrial drug design research departments, the number of FDA-approved new molecular entities per year stagnates, and the pharmaceutical industry is reorganising accordingly. The recent spate of industrial consolidations and the concomitant move towards outsourcing of research activities requires better integration of all activities along the chain from bench to bedside. The next 25 years will undoubtedly show a series of translational science activities that are aimed at a better communication between all parties involved, from quantum chemistry to bedside and from academia to industry. This will above all include understanding the underlying biological problem and optimal use of all available data.
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Affiliation(s)
| | - V. Lounnas
- CMBI, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26–28, 6525 GA Nijmegen, The Netherlands
| | - R. McGuire
- BioAxis Research, Bergse Heihoek 56, Berghem, 5351 SL The Netherlands
| | - T. van den Bergh
- Bio-Prodict, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | | | - L. Oliveira
- Sao Paulo Federal University (UNIFESP), Sao Paulo, Brazil
| | - G. Vriend
- CMBI, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26–28, 6525 GA Nijmegen, The Netherlands
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28
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Krüger DM, Bergs J, Kazemi S, Gohlke H. Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids. ACS Med Chem Lett 2011; 2:489-93. [PMID: 24900336 DOI: 10.1021/ml100217h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 04/06/2011] [Indexed: 11/28/2022] Open
Abstract
The highly flexible nature of RNA provides a formidable challenge for structure-based drug design approaches that target RNA. We introduce an approach for modeling target conformational changes in RNA-ligand docking based on potential grids that are represented as elastic bodies using Navier's equation. This representation provides an accurate and efficient description of RNA-ligand interactions even in the case of a moving RNA structure. When applied to a data set of 17 RNA-ligand complexes, filtered out of the largest validation data set used for RNA-ligand docking so far, the approach is twice as successful as docking into an apo structure and still half as successful as redocking to the holo structure. The approach allows considering RNA movements of up to 6 Å rmsd and is based on a uniform and robust parametrization of the properties of the elastic potential grids, so that the approach is applicable to different RNA-ligand complex classes.
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Affiliation(s)
- Dennis M. Krüger
- Department of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Johannes Bergs
- Department of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Sina Kazemi
- Department of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Department of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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29
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Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM. Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nat Chem Biol 2011; 7:553-9. [PMID: 21706033 PMCID: PMC3319144 DOI: 10.1038/nchembio.596] [Citation(s) in RCA: 213] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 04/18/2011] [Indexed: 11/09/2022]
Abstract
Current approaches used to identify protein-binding small molecules are not suited for identifying small molecules that can bind emerging RNA drug targets. By docking small molecules onto an RNA dynamic ensemble constructed by combining NMR spectroscopy and computational molecular dynamics, we virtually screened small molecules that target the entire structure landscape of the transactivation response element (TAR) from HIV type 1 (HIV-1). We quantitatively predict binding energies for small molecules that bind different RNA conformations and report the de novo discovery of six compounds that bind TAR with high affinity and inhibit its interaction with a Tat peptide in vitro (K(i) values of 710 nM-169 μM). One compound binds HIV-1 TAR with marked selectivity and inhibits Tat-mediated activation of the HIV-1 long terminal repeat by 81% in T-cell lines and HIV replication in an HIV-1 indicator cell line (IC(50) ∼23.1 μM).
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Affiliation(s)
- Andrew C. Stelzer
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Aaron T. Frank
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences 2, Irvine, California 92697, USA
| | - Jeremy D. Kratz
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Michael D. Swanson
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Marta J. Gonzalez-Hernandez
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Janghyun Lee
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences 2, Irvine, California 92697, USA
| | - David M. Markovitz
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Hashim M. Al-Hashimi
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
- Correspondence and requests for materials should be addressed to H. M. A. ()
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30
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Abstract
RNA molecules are involved in a wide range of biological processes and have been recognized as very important therapeutic targets. Mainly owing to the scarcity of information and experimental studies, the application of computational approaches and, in particular, of docking methodologies in the RNA field has developed slowly. However, in recent years the docking of RNA-binding ligands has experienced significant expansion. This article focuses attention on the docking of RNA-binding ligands, analyzing the development of RNA-docking approaches, the reliability of the docking methods and, finally, evaluating the results of docking-based virtual screening studies reported in the literature.
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31
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Ghemtio L, Devignes MD, Smaïl-Tabbone M, Souchet M, Leroux V, Maigret B. Comparison of three preprocessing filters efficiency in virtual screening: identification of new putative LXRbeta regulators as a test case. J Chem Inf Model 2010; 50:701-15. [PMID: 20420434 DOI: 10.1021/ci900356m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In silico screening methodologies are widely recognized as efficient approaches in early steps of drug discovery. However, in the virtual high-throughput screening (VHTS) context, where hit compounds are searched among millions of candidates, three-dimensional comparison techniques and knowledge discovery from databases should offer a better efficiency to finding novel drug leads than those of computationally expensive molecular dockings. Therefore, the present study aims at developing a filtering methodology to efficiently eliminate unsuitable compounds in VHTS process. Several filters are evaluated in this paper. The first two are structure-based and rely on either geometrical docking or pharmacophore depiction. The third filter is ligand-based and uses knowledge-based and fingerprint similarity techniques. These filtering methods were tested with the Liver X Receptor (LXR) as a target of therapeutic interest, as LXR is a key regulator in maintaining cholesterol homeostasis. The results show that the three considered filters are complementary so that their combination should generate consistent compound lists of potential hits.
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Affiliation(s)
- Léo Ghemtio
- Nancy Université, LORIA, Groupe ORPAILLEUR, Campus scientifique, BP 239, 54506 Vandoeuvre-les-Nancy Cedex, France.
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32
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Li Y, Shen J, Sun X, Li W, Liu G, Tang Y. Accuracy Assessment of Protein-Based Docking Programs against RNA Targets. J Chem Inf Model 2010; 50:1134-46. [DOI: 10.1021/ci9004157] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yaozong Li
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jie Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xianqiang Sun
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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33
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Fulle S, Gohlke H. Molecular recognition of RNA: challenges for modelling interactions and plasticity. J Mol Recognit 2010; 23:220-31. [PMID: 19941322 DOI: 10.1002/jmr.1000] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There is growing interest in molecular recognition processes of RNA because of RNA's widespread involvement in biological processes. Computational approaches are increasingly used for analysing and predicting binding to RNA, fuelled by encouraging progress in developing simulation, free energy and docking methods for nucleic acids. These developments take into account challenges regarding the energetics of RNA-ligand binding, RNA plasticity, and the presence of water molecules and ions in the binding interface. Accordingly, we will detail advances in force field and scoring function development for molecular dynamics (MD) simulations, free energy computations and docking calculations of nucleic acid complexes. Furthermore, we present methods that can detect moving parts within RNA structures based on graph-theoretical approaches or normal mode analysis (NMA). As an example of the successful use of these developments, we will discuss recent structure-based drug design approaches that focus on the bacterial ribosomal A-site RNA as a drug target.
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Affiliation(s)
- Simone Fulle
- Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany
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34
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Hyun S, Na J, Lee SJ, Park S, Yu J. RNA Grooves Can Accommodate Disulfide-Bridged Bundles of α-Helical Peptides. Chembiochem 2010; 11:767-70. [DOI: 10.1002/cbic.201000072] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (NEW YORK, N.Y.) 2009; 15:1219-30. [PMID: 19369428 PMCID: PMC2685511 DOI: 10.1261/rna.1563609] [Citation(s) in RCA: 552] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there is a need for the tools used in protein-based drug design, particularly DOCKing algorithms, to be extended or adapted for nucleic acids. Here, we have compiled a test set of RNA-ligand complexes to validate the ability of the DOCK suite of programs to successfully recreate experimentally determined binding poses. With the optimized parameters and a minimal scoring function, 70% of the test set with less than seven rotatable ligand bonds and 26% of the test set with less than 13 rotatable bonds can be successfully recreated within 2 A heavy-atom RMSD. When DOCKed conformations are rescored with the implicit solvent models AMBER generalized Born with solvent-accessible surface area (GB/SA) and Poisson-Boltzmann with solvent-accessible surface area (PB/SA) in combination with explicit water molecules and sodium counterions, the success rate increases to 80% with PB/SA for less than seven rotatable bonds and 58% with AMBER GB/SA and 47% with PB/SA for less than 13 rotatable bonds. These results indicate that DOCK can indeed be useful for structure-based drug design aimed at RNA. Our studies also suggest that RNA-directed ligands often differ from typical protein-ligand complexes in their electrostatic properties, but these differences can be accommodated through the choice of potential function. In addition, in the course of the study, we explore a variety of newly added DOCK functions, demonstrating the ease with which new functions can be added to address new scientific questions.
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Affiliation(s)
- P Therese Lang
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94143, USA
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36
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Pinto IG, Guilbert C, Ulyanov NB, Stearns J, James TL. Discovery of ligands for a novel target, the human telomerase RNA, based on flexible-target virtual screening and NMR. J Med Chem 2009; 51:7205-15. [PMID: 18950148 DOI: 10.1021/jm800825n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human ribonucleoprotein telomerase is a validated anticancer drug target, and hTR-P2b is a part of the human telomerase RNA (hTR) essential for its activity. Interesting ligands that bind hTR-P2b were identified by iteratively using a tandem structure-based approach: docking of potential ligands from small databases to hTR-P2b via the program MORDOR, which permits flexibility in both ligand and target, with subsequent NMR screening of high-ranking compounds. A high percentage of the compounds tested experimentally were found via NMR to bind to the U-rich region of hTR-P2b; most have MW < 500 Da and are from different compound classes, and several possess a charge of 0 or +1. Of the 48 ligands identified, 24 exhibit a decided preference to bind hTR-P2b RNA rather than A-site rRNA and 10 do not bind A-site rRNA at all. Binding affinity was measured by monitoring RNA imino proton resonances for some of the compounds that showed hTR binding preference.
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Affiliation(s)
- Irene Gómez Pinto
- Department of Pharmaceutical Chemistry, MC 2280, University of Californias San Francisco, 600 16th Street, San Francisco, California 94158-2517, USA
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37
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Nicola G, Abagyan R. Structure-based approaches to antibiotic drug discovery. ACTA ACUST UNITED AC 2009; Chapter 17:Unit17.2. [PMID: 19235149 DOI: 10.1002/9780471729259.mc1702s12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of antimicrobials has advanced tremendously over the past century. However, as our production capacity increases, the threat of resistance is ever-present. To combat this resistance, two main avenues of drug discovery are being pursued: identifying new microbial proteins for which to direct drug discovery efforts, and designing innovative drugs that target existing proteins. The advent of structural genomics research has advanced to the point of rapidly discovering novel microbial protein targets. In addition, modern tools of computational biology greatly enhance the speed and reliability of antimicrobial discovery. The various steps of this process are outlined and discussed, including virtual ligand screening, pocket identification, and compound optimization.
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Affiliation(s)
- George Nicola
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
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38
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Guilbert C, James TL. Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. J Chem Inf Model 2008; 48:1257-68. [PMID: 18510306 DOI: 10.1021/ci8000327] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based drug design is now well-established for proteins as a key first step in the lengthy process of developing new drugs. In many ways, RNA may be a better target to treat disease than a protein because it is upstream in the translation pathway, so inhibiting a single mRNA molecule could prevent the production of thousands of protein gene products. Virtual screening is often the starting point for structure-based drug design. However, computational docking of a small molecule to RNA seems to be more challenging than that to protein due to the higher intrinsic flexibility and highly charged structure of RNA. Previous attempts at docking to RNA showed the need for a new approach. We present here a novel algorithm using molecular simulation techniques to account for both nucleic acid and ligand flexibility. In this approach, with both the ligand and the receptor permitted some flexibility, they can bind one another via an induced fit, as the flexible ligand probes the surface of the receptor. A possible ligand can explore a low-energy path at the surface of the receptor by carrying out energy minimization with root-mean-square-distance constraints. Our procedure was tested on 57 RNA complexes (33 crystal and 24 NMR structures); this is the largest data set to date to reproduce experimental RNA binding poses. With our procedure, the lowest-energy conformations reproduced the experimental binding poses within an atomic root-mean-square deviation of 2.5 A for 74% of tested complexes.
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Affiliation(s)
- Christophe Guilbert
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
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39
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Park SJ, Jung YH, Kim YG, Park HJ. Identification of novel ligands for the RNA pseudoknot that regulate -1 ribosomal frameshifting. Bioorg Med Chem 2008; 16:4676-84. [PMID: 18321712 PMCID: PMC7125880 DOI: 10.1016/j.bmc.2008.02.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 02/05/2008] [Accepted: 02/08/2008] [Indexed: 11/24/2022]
Abstract
In many viruses, -1 ribosomal frameshifting (-1RF) regulates synthesis of proteins and is crucial for virus production. An RNA pseudoknot is one of the essential components of the viral -1RF system. Thermodynamic or kinetic control of pseudoknot folding may be important in regulating the efficiency of -1RF. Thus, small molecules that interact with viral RNA pseudoknots may disrupt the -1RF system and show antiviral activity. In this study, we conducted virtual screening of a chemical database targeting the X-ray crystal structure of RNA pseudoknot complexed with biotin to identify ligands that may regulate an -1RF system containing biotin-aptamer as an RNA pseudoknot component. After docking screening of about 80,000 compounds, 58 high-ranked hits were selected and their activities were examined by in vitro and cell-based -1 frameshifting assays. Six compounds increased the efficiency of -1 frameshifting, and these are novel small molecule compounds that regulate the -1RF.
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Affiliation(s)
- So-Jung Park
- College of Pharmacy, Sungkyunkwan University, Suwon 440-746, Republic of Korea
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40
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Pfeffer P, Gohlke H. DrugScoreRNA--knowledge-based scoring function to predict RNA-ligand interactions. J Chem Inf Model 2007; 47:1868-76. [PMID: 17705464 DOI: 10.1021/ci700134p] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is growing interest in RNA as a drug target due to its widespread involvement in biological processes. To exploit the power of structure-based drug-design approaches, novel scoring and docking tools need to be developed that can efficiently and reliably predict binding modes and binding affinities of RNA ligands. We report for the first time the development of a knowledge-based scoring function to predict RNA-ligand interactions (DrugScoreRNA). Based on the formalism of the DrugScore approach, distance-dependent pair potentials are derived from 670 crystallographically determined nucleic acid-ligand and -protein complexes. These potentials display quantitative differences compared to those of DrugScore (derived from protein-ligand complexes) and DrugScoreCSD (derived from small-molecule crystal data). When used as an objective function for docking 31 RNA-ligand complexes, DrugScoreRNA generates "good" binding geometries (rmsd (root mean-square deviation) < 2 A) in 42% of all cases on the first scoring rank. This is an improvement of 44% to 120% when compared to DrugScore, DrugScoreCSD, and an RNA-adapted AutoDock scoring function. Encouragingly, good docking results are also obtained for a subset of 20 NMR structures not contained in the knowledge-base to derive the potentials. This clearly demonstrates the robustness of the potentials. Binding free energy landscapes generated by DrugScoreRNA show a pronounced funnel shape in almost 3/4 of all cases, indicating the reduced steepness of the knowledge-based potentials. Docking with DrugScoreRNA can thus be expected to converge fast to the global minimum. Finally, binding affinities were predicted for 15 RNA-ligand complexes with DrugScoreRNA. A fair correlation between experimental and computed values is found (RS = 0.61), which suffices to distinguish weak from strong binders, as is required in virtual screening applications. DrugScoreRNA again shows superior predictive power when compared to DrugScore, DrugScoreCSD, and an RNA-adapted AutoDock scoring function.
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Affiliation(s)
- Patrick Pfeffer
- Department of Biological Sciences, Molecular Bioinformatics Group, J.W. Goethe-University, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
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41
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Yan Z, Sikri S, Beveridge DL, Baranger AM. Identification of an aminoacridine derivative that binds to RNA tetraloops. J Med Chem 2007; 50:4096-104. [PMID: 17665894 DOI: 10.1021/jm070305p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA folds into diverse structures that form unique targets for small molecules and thus provide significant potential for controlling biological processes involving RNA with small-molecule ligands. We are investigating molecular recognition of tetraloop RNA by small molecules. RNA tetraloops are four-nucleotide stem loops with unusual stability that are involved in biological processes involving RNA by forming binding sites for proteins and other RNAs. We have sequentially used the docking programs DOCK and AutoDock to screen 1990 small molecules in the NCI diversity set to identify molecules selective for RNA tetraloops over double-stranded RNA. The compounds predicted to bind to tetraloop RNA were evaluated for binding RNA tetraloops using 1H NMR spectroscopy and fluorescence techniques. An aminoacridine derivative (AD2) was identified that binds to a GAAA tetraloop in a 2:1 ratio with dissociation constants of 1.0 and 4.0 microM. AD2 binds with approximately 20-fold and 9-fold higher affinity to tetraloop RNA than to double- and single-stranded RNAs, respectively.
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Affiliation(s)
- Zhaohui Yan
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
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42
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Klebe G. Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 2007; 11:580-94. [PMID: 16793526 PMCID: PMC7108249 DOI: 10.1016/j.drudis.2006.05.012] [Citation(s) in RCA: 459] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 02/13/2006] [Accepted: 05/16/2006] [Indexed: 11/28/2022]
Abstract
In contrast to high-throughput screening, in virtual ligand screening (VS), compounds are selected using computer programs to predict their binding to a target receptor. A key prerequisite is knowledge about the spatial and energetic criteria responsible for protein–ligand binding. The concepts and prerequisites to perform VS are summarized here, and explanations are sought for the enduring limitations of the technology. Target selection, analysis and preparation are discussed, as well as considerations about the compilation of candidate ligand libraries. The tools and strategies of a VS campaign, and the accuracy of scoring and ranking of the results, are also considered.
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Affiliation(s)
- Gerhard Klebe
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35032 Marburg, Germany.
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43
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Moitessier N, Westhof E, Hanessian S. Docking of aminoglycosides to hydrated and flexible RNA. J Med Chem 2006; 49:1023-33. [PMID: 16451068 DOI: 10.1021/jm0508437] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although much effort has been devoted to the development of programs suited for the docking of ligands to proteins, much less progress has been achieved in the nucleic acid field. We have developed a unique approach for docking aminoglycosides to RNA considering the flexibility of these macromolecules using conformational ensembles and accounting for the role of the first hydration shell. This concept, successfully implemented in AutoDock, relies on the computation of the intermolecular interaction energy that accounts for the presence of dynamically bound water molecules to the RNA. As an application, a set of 11 aminoglycosides was docked with an average root-mean-square deviation (RMSD) of 1.41 A to be compared with an average RMSD of 3.25 A when the original AutoDock protocol was used.
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Affiliation(s)
- Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 2K6, Canada.
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44
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Han LY, Lin HH, Li ZR, Zheng CJ, Cao ZW, Xie B, Chen YZ. PEARLS: Program for Energetic Analysis of Receptor−Ligand System. J Chem Inf Model 2006; 46:445-50. [PMID: 16426079 DOI: 10.1021/ci0502146] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analysis of the energetics of small molecule ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions facilitates the quantitative understanding of molecular interactions that regulate the function and conformation of proteins. It has also been extensively used for ranking potential new ligands in virtual drug screening. We developed a Web-based software, PEARLS (Program for Energetic Analysis of Ligand-Receptor Systems), for computing interaction energies of ligand-protein, ligand-nucleic acid, protein-nucleic acid, and ligand-protein-nucleic acid complexes from their 3D structures. AMBER molecular force field, Morse potential, and empirical energy functions are used to compute the van der Waals, electrostatic, hydrogen bond, metal-ligand bonding, and water-mediated hydrogen bond energies between the binding molecules. The change in the solvation free energy of molecular binding is estimated by using an empirical solvation free energy model. Contribution from ligand conformational entropy change is also estimated by a simple model. The computed free energy for a number of PDB ligand-receptor complexes were studied and compared to experimental binding affinity. A substantial degree of correlation between the computed free energy and experimental binding affinity was found, which suggests that PEARLS may be useful in facilitating energetic analysis of ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions. PEARLS can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/rune.pl.
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Affiliation(s)
- L Y Han
- Department of Computational Science, National University of Singapore, Singapore
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45
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Alonso H, Bliznyuk AA, Gready JE. Combining docking and molecular dynamic simulations in drug design. Med Res Rev 2006; 26:531-68. [PMID: 16758486 DOI: 10.1002/med.20067] [Citation(s) in RCA: 456] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from genomic and proteomic initiatives, and from the large libraries of small compounds now readily available through combinatorial chemistry. Despite a shaky early history, computer-aided drug design techniques can now be effective in reducing costs and speeding up drug discovery. This happy outcome results from development of more accurate and reliable algorithms, use of more thoughtfully planned strategies to apply them, and greatly increased computer power to allow studies with the necessary reliability to be performed. Our review focuses on applications and protocols, with the main emphasis on critical analysis of recent studies where docking calculations and molecular dynamics (MD) simulations were combined to dock small molecules into protein receptors. We highlight successes to demonstrate what is possible now, but also point out drawbacks and future directions. The review is structured to lead the reader from the simpler to more compute-intensive methods. Thus, while inexpensive and fast docking algorithms can be used to scan large compound libraries and reduce their size, more accurate but expensive MD simulations can be applied when a few selected ligand candidates remain. MD simulations can be used: during the preparation of the protein receptor before docking, to optimize its structure and account for protein flexibility; for the refinement of docked complexes, to include solvent effects and account for induced fit; to calculate binding free energies, to provide an accurate ranking of the potential ligands; and in the latest developments, during the docking process itself to find the binding site and correctly dock the ligand a priori.
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Affiliation(s)
- Hernán Alonso
- Computational Proteomics Group, John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
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46
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Agbottah E, Zhang N, Dadgar S, Pumfery A, Wade JD, Zeng C, Kashanchi F. Inhibition of HIV-1 virus replication using small soluble Tat peptides. Virology 2005; 345:373-89. [PMID: 16289656 DOI: 10.1016/j.virol.2005.09.062] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 07/19/2005] [Accepted: 09/30/2005] [Indexed: 11/17/2022]
Abstract
Although the introduction of highly active antiretroviral therapy (HAART) has led to a significant reduction in AIDS-related morbidity and mortality, unfortunately, many patients discontinue their initial HAART regimen, resulting in development of viral resistance. During HIV infection, the viral activator Tat is needed for viral progeny formation, and the basic and core domains of Tat are the most conserved parts of the protein. Here, we show that a Tat 41/44 peptide from the core domain can inhibit HIV-1 gene expression and replication. The peptides are not toxic to cells and target the Cdk2/Cyclin E complex, inhibiting the phosphorylation of serine 5 of RNAPII. Using the Cdk2 X-ray crystallography structure, we found that the low-energy wild-type peptides could bind to the ATP binding pocket, whereas the mutant peptide bound to the Cdk2 interface. Finally, we show that these peptides do not allow loading of the catalytic domain of the cdk/cyclin complex onto the HIV-1 promoter in vivo.
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Affiliation(s)
- Emmanuel Agbottah
- Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington DC 20037, USA.
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47
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Renner S, Ludwig V, Boden O, Scheffer U, Göbel M, Schneider G. New inhibitors of the Tat-TAR RNA interaction found with a "fuzzy" pharmacophore model. Chembiochem 2005; 6:1119-25. [PMID: 15883975 DOI: 10.1002/cbic.200400376] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
TAR RNA is a potential target for AIDS therapy. Ligand-based virtual screening was performed to retrieve novel scaffolds for RNA-binding molecules capable of inhibiting the Tat-TAR interaction, which is essential for HIV replication. We used a "fuzzy" pharmacophore approach (SQUID) and an alignment-free pharmacophore method (CATS3D) to carry out virtual screening of a vendor database of small molecules and to perform "scaffold-hopping". A small subset of 19 candidate molecules were experimentally tested for TAR RNA binding in a fluorescence resonance energy transfer (FRET) assay. Both methods retrieved molecules that exhibited activities comparable to those of the reference molecules acetylpromazine and chlorpromazine, with the best molecule showing ten times better binding behavior (IC50 = 46 microM). The hits had molecular scaffolds different from those of the reference molecules.
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Affiliation(s)
- Steffen Renner
- Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Johann-Wolfgang-Goethe-Universität, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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48
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Pitt SW, Zhang Q, Patel DJ, Al-Hashimi HM. Evidence that Electrostatic Interactions Dictate the Ligand-Induced Arrest of RNA Global Flexibility. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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49
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Pitt SW, Zhang Q, Patel DJ, Al-Hashimi HM. Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility. Angew Chem Int Ed Engl 2005; 44:3412-5. [PMID: 15861447 PMCID: PMC4690522 DOI: 10.1002/anie.200500075] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephen W. Pitt
- Department of Pharmacology, Weil Medical College of Cornell University, New York, NY 10021 (USA)
| | - Qi Zhang
- Department of Chemistry and Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109 (USA), Fax: (+1)734-647-4865
| | - Dinshaw J. Patel
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021 (USA)
| | - Hashim M. Al-Hashimi
- Department of Chemistry and Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109 (USA), Fax: (+1)734-647-4865
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50
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Morley SD, Afshar M. Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock. J Comput Aided Mol Des 2005; 18:189-208. [PMID: 15368919 DOI: 10.1023/b:jcam.0000035199.48747.1e] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.
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Affiliation(s)
- S David Morley
- RiboTargets, Granta Park, Abington, Cambridgeshire CBI 6GB, UK.
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